Microbial flavo-hydroxylases catalyze the hydroxylation of various organic molecules, including toxicants and pollutants, rendering the products suitable for further biodegradation. The present work centers at the elucidation of catalytic mechanisms and activity regulations, both in vitro and in vivo, of two flavo-hydroxylases, namely salicylate hydroxylase and bacterial luciferase. An oxygenated flavin - luciferase intermediate - has been stabilized, isolated, and characterized with respect to spectral, physicochemical and catalytic properties. The formation and isolation of such intermediates formed with various flavin derivatives are under current investigations. The kinetics of bacterial bioluminescence in vivo have been studied. The rate-limiting step is most likely the formation of excited emitter, in agreement with previous in vitro studies. Salicylate hydroxylase exhibits oxidase/monooxygenase dual activities, which are subject to differential regulations by organic co-solvents, medium dielectric constants, and flavins. The induction of multiple hydroxylase species in Pseudomonas cepacia has been observed.